Gower Algorithm Research Articles

Genetic Diversity of Common Bean (Phaseolus vulgaris L.) Landraces Based on Morphological Traits and Molecular Markers.

The objective of this study was to evaluate the genetic diversity among traditional common bean accessions through morphological descriptors and molecular markers. Sixty-seven common bean accessions from the Germplasm bank of the Instituto Federal of Espírito Santo-Campus de Alegre were evaluated. For this, 25 specific morphological descriptors were used, namely 12 quantitative and 13 qualitative ones. A diversity analysis based on morphological descriptors was carried out using the Gower algorithm. For molecular characterization, 23 ISSR primers were used to estimate dissimilarity using the Jaccard Index. Based on the dendrograms obtained by the UPGMA method, for morphological and molecular characterization, high genetic variability was observed between the common bean genotypes studied, evidenced by cophenetic correlation values in the order of 0.99, indicating an accurate representation of the dissimilarity matrix by the UPGMA clustering. In the morphological characterization, high phenotypic diversity was observed between the accessions, with grains of different shapes, colors, and sizes, and the accessions were grouped into nine distinct groups. Molecular characterization was efficient in separating the genotypes in the Andean and Mesoamerican groups, with the 23 ISSR primers studied generating an average of 6.35 polymorphic bands. The work identified divergent accessions that can serve different market niches, which can be indicated as parents to form breeding programs in order to obtain progenies with high genetic variability.

Categories of variables in analysis of genetic diversity in S1 progenies of Psidium guajava

Crossing and developing inbred lines have been promising options for guava breeding programs. The purpose of this study was to evaluate the genetic divergence among genotypes of S1 inbred guava families by means of the Gower’s technique and the Ward-MLM methodology, to verify the correlation and relative contribution of traits, as well as to identify descriptors with minimum efficiency for this species. The experiment was implemented at the Estação Experimental da Ilha Barra do Pomba, in the municipality of Itaocara, RJ, Brazil. A randomized block design with 18 inbred families, three replicates, and ten plants per plot was used for the experimental design. After 19 months from the planting of the experiment, the 61 earliest and most productive genotypes (individual plants) were evaluated. For this purpose, 29 descriptors were evaluated, of which fifteen were qualitative and fourteen, quantitative. The characteristics required to obtain the distance matrix were analyzed based on the Gower algorithm, and a comparative cluster between the dendrograms of the morphoagronomic variables was achieved from this matrix. Lastly, the Ward-MLM procedure was applied to form the clusters of inbred families. By using all 29 descriptors, greater efficiency was achieved in cluster discrimination. Hence, according to the results identified, it is not possible to indicate minimum descriptors for the culture. Using the Ward-MLM method, the descriptors that most contributed to the divergence among the genotypes were fruit flesh mass, fruit weight, fruit diameter, fruit flesh thickness, fruit placental mass, and fruit length. The most divergent genotypes can be recommended for further crosses or self-pollinations to develop new lines in the guava breeding program of UENF.

Phenotypic divergence among half-sib progenies of African mahogany.

Divergence studies are essential for the conservation of genetic resources and guidance in genetic improvement programs. This study aimed to assess the phenotypic dispersion of half-sib progenies using Gower's algorithm and the non-metric multidimensional scaling analysis based on qualitative and quantitative traits. Twenty-two half-sib progenies of African mahogany (Khaya senegalensis) were evaluated in a randomized block design with 22 treatments (progenies/origin), with 30 replications and one plant per plot, totaling 660 plants. The total tree height (cm), diameter at soil level (cm), chlorophyll A and B, presence of bifurcation, presence of lateral branches, stem tortuosity, and the phytosanitary and nutritional status according to a rating scale were evaluated. Data analysis was performed at the progeny mean level for the quantitative traits and the modal value was used for the qualitative traits. The technique used presented the distance between the progenies of K. senegalensis in a graphical form. The dispersion of the progenies in the graph is indicative that there is phenotypic variation in the progeny test, allowing to select individuals with characteristics of interest to improve mahogany for Piauí. Gower's algorithm applied to mixed data and non-metric multidimensional scaling are efficient methods to describe phenotypic similarities between progenies.

Characterization of strawberry genotypes with low chilling requirement for cultivation in tropical regions

Although strawberry can be cultivated in all types of climate, it grows best in temperate climates, limiting its cultivation in certain countries or regions with tropical or subtropical climates. The objective of this study was to verify the genetic diversity of 34 pre-selected day-neutral strawberry genotypes in humid tropical and subtropical conditions through characterization of morpho-agronomic characteristics and molecular markers. The selection was based on qualitative and quantitative morpho-agronomic traits, using the Gower algorithm. Molecular characterization was performed with AFLP markers, using four combinations of selective primers. Six representative variables were subjected to principal component analysis (PCA) and the Mulamba and Mock selection index. Soluble solids and luminosity of the outer part of the fruit did not differ among genotypes but presented values ​​above those usually found. AFLP markers detected 80% polymorphism, confirming high genetic variability among genotypes. Clustering based on molecular and agronomic data separated the genotypes into three groups, and the Mulamba and Mock index did not select individuals derived from 'Albion' or RVFS06. PCA highlighted the genotypes RVCA16M-1, RVDA11M-3, RVDA11M-4, and RVDA11M-25 as superior for most of the evaluated traits compared with the commercial cultivars 'Albion' and 'Monterey'. The PCA and selection index results indicate the reliability of the multivariate analysis for selecting superior strawberry genotypes for cultivation in tropical regions. Of the 34 genotypes analyzed, four stood out with potential for immediate cultivation.

Research Article Estimate of genetic diversity in germplasm of elephant grass accessions in Brazil using the Gower algorithm

Research Article Estimate of genetic diversity in germplasm of elephant grass accessions in Brazil using the Gower algorithm

Phenotypic variability of cowpea genotypes for immature seed harvesting

ABSTRACT Seed color, brightness and texture are important aspects for the consumption of immature beans. This study aimed to estimate the phenotypic variability among thirty cowpea genotypes for immature seed harvesting, in order to guide breeding programs. The experiment was carried out in a randomized blocks design, with three replications. The evaluated traits were immature seeds yield, pods and dry seeds production, number of immature pods, 100-immature seeds weight, immature pods length, number of seeds per immature pod, cooking time, harvesting period of immature pods, seed color, pod color, plant growth habit, opening of immature pods, seed threshing from immature pods, cultivation value and seed browning after threshing. Anova and three clustering methods were applied: UPGMA using the Jaccard coefficient of similarity; modified Tocher method based on the Gower algorithm; and k-means. All the analyses were performed based on the variable means of experiments evaluated in six environments. A statistically significant phenotypic variability was observed among all the quantitative traits. Discrepancies occurred in the accessions grouping and number of clusters. The accession BRS Acauã, in one group, and P508 and PCCR3F6L15, in other groups, showed a good quality for immature grain harvesting, were consistently grouped into different clusters and are recommended for use as parents in the development of new cultivars.

Backcrosses in a segregating population of Passiflora mediated by morphoagronomic and resistance traits

ABSTRACT The present study aims to characterize the genetic diversity of Passiflora setacea, P. edulis, their hybrids, and first-backcross progenies, and to indicate promising recombinants for generation advancement in a breeding program for transferring resistance to cowpea aphid-borne mosaic virus (CABMV). Ninety-one genotypes were evaluated for 37 morphoagronomic descriptors. The traits were analyzed to obtain a distance matrix, based on the Gower algorithm, using the Ward-Modified Location Model (MLM) procedure for the composition of genetic groups. The adopted strategy led to the formation of five homogeneous groups, where groups I, III, and V comprised the parents P. setacea, P. edulis and interspecific hybrids, respectively, while groups II and IV consisted of 69 genotypes of BC1. Broad variability was observed among the tested genotypes, and the highest was shown by group IV. Genotypes 17, 293, 355, and 501, from group IV, were the most promising for the second backcross cycle as they showed good resistance to the disease and desirable morphoagronomictraits.

DIVERSIDADE GENÉTICA ENTRE ACESSOS DE SOJA TIPO ALIMENTO COM BASE NO ALGORITMO DE GOWER

The simultaneous evaluation of qualitative and quantitative traits is an excellent tool to estimate the genetic divergence among accessionsof germplasm banks. The present study aimedto characterize and estimatethe genetic divergence among soybean food type accessionsbased on Gower algorithm and identifies promising combination among accessionsevaluated. A total of 64 soybean genotypes were studied, which 60arefood type soybean accessions, twoarecommercial cultivars also for human consumption,and two are grain type commercial cultivars. Three qualitative and seven quantitativetraits were used to estimate the genetic divergence among genotypes. The experiment was carried out in the experimental areaof the Universidade Estadual de Londrina during 2015/2016season, using a randomized complete block design with four repetitions. It was observed the presence of genetic variability to all traits evaluated. Thegrainyield trait was the mostefficientin discriminating theevaluated accessions,while plant height showed lower contribution. The UPGMA method showed the highestcoefficient of cophenetic correlation allowing the formation of six different groups. The crossings AL06 × AL22 and AL07 × AL22 are promising for obtaining superior genotypes destined to the in naturaconsumption and production of soy milk and tofu. The combination AL13 × AL60 is considered favorable for obtaining genotypes destined to natto production. The use of the AL12 and AL13 accessions as parents is advantageous for obtaining genotypes for the production of kuroname.

Intra- and interspecific genetic divergence in Macroptilium (Benth.) Urb.: a forage option for Brazilian semiarid

The objective of this study was to characterize and quantify the genetic diversity within and between species of the genus Macroptilium with potential in animal feed, through morpho-agronomic descriptors. Sixty-four accessions of three species were used. The experimental design was randomized block design with three replications and five plants per plot. Eighteen qualitative and six quantitative morphological descriptors were used in addition to six agronomic descriptors. Quantitative data were submitted to analysis of variance and means were compared by Scott–Knott test, at 5% significance. For the divergence analyzes all the descriptors were grouped based on the Gower algorithm. The dendrogram was obtained by the UPGMA hierarchical grouping method and the relative importance of the characters was calculated for the divergence. There was significant effect for most quantitative traits and high variability for both between and within the studied species. Seven groups were formed which were grouped mainly in relation to the species. Groups IV, VI and VIII formed by accessions of M. atropurpureum (Sesse and Moc. ex DC.) Urb. have characteristics of interest for animal feeding. CTM-S04 and CTM-S07, not taxonomically classified, were allocated to these groups. The accessions that presented the greatest potential for animal production were CTM-A16 and CTM-M8, because they presented high dry matter production and high leaf:stem ratio. These accessions were superior to the cultivar Siratro (CTM-A27) with respect to these descriptors. These results indicate that the genotypes showed variability between and within the species which make possible their use in programs of selection and breeding for animal feed.

Estimative of genetic diversity in germ-plasm of elephant grass using the Gower algorithm

This work aimed at estimating the genetic divergence among 85 accessions of elephant-grass using the Gower algorithm for the joint study of quantitative and qualitative traits. The experiment was conducted in the city of Campos dos Goytacazes, Rio de Janeiro state, Brazil, with of 85 elephant-grass genotypes. It was applied a randomized block experimental design with two replications. The experimental unit consisted of one 5.5 m-line with spacing of 2 m, totaling 11 m2. The plot area was a sampling at the center of the plot. Morpho-agronomic, multi-categorical, and phenological traits were assessed. The estimation of the genetic distance matrix was carried out by means of the joint analysis of the quantitative and qualitative variables obtained based on the Gower algorithm. The data were analyzed using GENES and R program. The results revealed that there is a wide genetic variability among the accessions studied. Some accessions show low genetic distances, which indicates that they are duplicates in the germplasm bank.

BUFFEL GRASS MORPHOAGRONOMIC CHARACTERIZATION FROM Cenchrus GERMPLASM ACTIVE BANK

ABSTRACT This study aimed to characterize buffel grass accessions of the Cenchrus Germplasm Active Bank (CGAB) from Embrapa Semi-Arid in a morphoagronomic way, checking the descriptors variability and efficiency in accessions on two consecutive cuts. Twenty-five accessions and five buffel grass cultivars were used in randomized complete block design with three replications. Evaluations were conducted after two consecutive cuts, each evaluation performed 90 days after each cut. Characterization was based on 15 quantitative and qualitative morphoagronomic descriptors. Quantitative descriptors were subjected to individual and joint univariate analysis of variance, followed by the Scott-Knott’s test at 5% significance. Yet qualitative descriptors were submitted to descriptive analysis. Both quantitative and qualitative descriptors were grouped based on the Gower algorithm for divergence analysis. A dendrogram and calculations of the characters relative importance for divergence were established. Genotype and cutting effects were significant for almost all descriptors in the joint analysis. This result indicates a genetic variability between genotypes and, regarding the cut, it indicates mainly differences in growth rate of each genotype in each cutting season. Genotypes were separated into three groups, which showed good genotype variation. The number of tillers per clump, followed by number of inflorescence and color of seeds, were the most relevant characters in genotype separation.

Multiple genetic resistances in Capsicum spp.

This study aimed to identify Capsicum genotypes with resistance to bacterial spot (BS), anthracnose and Pepper yellow mosaic virus (PepYMV). Fifty-four genotypes of Capsicum spp were evaluated. Resistance reaction against BS was evaluated using three replicates, testing hypersensitivity and quantitative resistance in leaves. After evaluation, inoculated leaves were detached from the plants, being then cultivated until reproductive stage for evaluations anthracnose resistance in immature and mature fruit, totalizing 18 fruits per genotype. For PepYMV resistance was performed with five replications. Each genotype reaction was evaluated by a scoring scale, using the area under the disease progress curve for each pathosystem, and incubation period for the three systems. The latent period was evaluated only for the pathosystem Capsicum-Colletotrichum gloeosporioides. Means were grouped by the Scott-Knott test. Measures of dissimilarity matrix among the genotypes were obtained by Gower's algorithm and the grouping was obtained by the UPGMA clustering method. The accessions belonging to the Capsicum frutescens were the most susceptible to the three diseases. At least one genotype of Capsicum baccatum var. pendulum, Capsicum annuum, and Capsicum chinense showed resistance potential to BS and PepYMV, for use in breeding programs. The accession UENF 1381 (C. annuum) was resistant to the three pathogens.

Morphological descriptors and ISSR molecular markers in the evaluation of genetic variability of Tectona grandis genotypes.

This study aimed to evaluate the genetic variability of the teak germplasm bank, using morphological traits and inter-simple sequence repeat molecular markers. Thirty clones were evaluated in a randomized complete block design with three replicates, and each plot was composed of three plants. A joint analysis of quantitative and qualitative variables was performed using the Gower algorithm. Quantitative, qualitative, and molecular variables were analyzed simultaneously using the Ward-MLM procedure. There is genetic variability among the 30 teak genotypes studied, considering the quantitative, qualitative, and molecular variables by the Ward-MLM statistical procedure. Morphological traits used proved to be efficient for the study of genetic variability; however, it was not possible to compose a descriptor table for clonal teak genotypes based on the traits evaluated. The Gower method was efficient in discriminating the groups, demonstrating that the simultaneous analysis of qualitative and quantitative data is feasible and can allow greater efficiency in the knowledge of the variability among teak genotypes. The genotype 22 showed to be the most divergent compared to the other genotypes, except for the cluster of genotypes by the UPGMA method based on the Gower distance obtained by the Ward-MLM procedure, which formed a group with genotypes 9 and 30, in the morphological and molecular analyses and was grouped alone.

<b>Clonal evaluation of new ornamental pineapple hybrids to use as cut flowers

Embrapa Cassava and Fruits has developed ornamental pineapple hybrids for several categories of ornamental use including cut flowers, potted plants and landscaping. The objective of this study was to carry out a clonal evaluation of two ornamental hybrids using quantitative and qualitative morphological descriptors to recommend these hybrids as new ornamental pineapple cultivars. Twenty plants of each hybrid (PL01 and PL04) were evaluated regarding the response to floral induction as well as the stability and homogeneity of the clones in two production cycles. The descriptive statistics were calculated and analyzed to determine the genetic distance based on the Gower algorithm. Four groups were formed, two using parental data and the other two containing the different hybrids that were evaluated in the two growing cycles. In the floral evaluation, the time from field planting to harvest of the stem as a cut flower was determined to be as long as 17 months in the first cycle and 13.5 months in the second cycle for both hybrids. They were characterized as a novelty in the flower market; they showed genetic stability and homogeneity and can be recommended as new cultivars of ornamental pineapple because they exhibit satisfactory quality and meet the market requirements.

English

The descriptors used to differentiate new soybean cultivars which ensure their protection, has become insufficient. This makes evident the need to expand the list of that already used. The morphological traits that may be used as descriptors can be quantitative or qualitative; however, in the evaluation of their efficiency, they are not always analyzed simultaneously. Thus, this study aimed to identify new morphological characteristics for purposes of discrimination of soybean cultivars with the aid of Gower algorithm, which allows evaluation of quantitative and qualitative characters simultaneously. Ten soybean cultivars were used in two experiments, one in the summer and another in the winter. They were conducted in a greenhouse. The experiments were carried out in an experimental randomized complete block design with four replications. Each experimental unit consisted of one pot with two plants. Five quantitative and seventeen qualitative characteristics were evaluated and the discrimination analysis was performed by Gower algorithm. It was concluded that there are differences among cultivars for all traits analyzed in both sowing dates, except for the opening of the petioles of the unifoliolate leaves. The use of Gower algorithm was efficient in the evaluation of discriminatory capacity of quantitative and qualitative characteristics simultaneously, demonstrating that they are useful as soybean descriptors. Key words: Glycine max (L.), law on plant variety protection, productivity, qualitative variables.

Genetic divergence through joint analysis of morphoagronomic and molecular characters in accessions of Jatropha curcas.

The aim of this study was to investigate the genetic divergence between accessions of Jatropha curcas through joint analysis of morphoagronomic and molecular characters. To this end, we investigated 11 morphoagronomic characters and performed molecular genotyping, using 23 inter-simple sequence repeat (ISSR) primers in 46 accessions of J. curcas. We calculated the contribution of each character on divergence using analysis of variance. The grouping among accessions was performed using the Ward-MLM (modified location model) method, using morphoagronomic and molecular data, whereas the cophenetic correlation was obtained based on Gower's algorithm. There were significant differences in all growth-related characteristics: number of primary and secondary branches per plant, plant height, and stem diameter. For characters related to grain production, differences were found for number of fruit clusters per plant and number of inflorescence clusters per plant and average number of seeds per fruit. The greatest phenotypic variation was found in plant height (59.67- 222.33 cm), whereas the smallest variation was found in average number of seeds per fruit (0-2.90), followed by the number of fruit clusters per plant (0-8.67). In total, 94 polymorphic ISSR fragments were obtained. The genotypic grouping identified six groups, indicating that there is genetic divergence among the accessions. The most promising crossings for future hybridization were identified among accessions UFRB60 and UFVJC45, and UFRB61 and UFVJC18. In conclusion, the joint analysis of morphoagronomic characters and ISSR markers is an efficient method to assess the genetic divergence in J. curcas.

Genetic dissimilarity and selection of putative mutants of Terra Maranhão plantain cultivar using the Ward-MLM strategy.

The objective of this study was to evaluate genetic variability and select putative mutants of Terra Maranhão plantain cultivar (AAB genome) subjected to gamma radiation based on agronomic data and inter simple sequence repeat molecular marker profiles using the Ward-MLM strategy. A total of 233 irradiated plants and 41 controls were assessed. The agronomic and molecular data were subjected to the Ward-MLM statistical algorithm in the SAS program. Cluster analysis was performed by the average distance method (UPGMA), based on the distance matrix of the Gower algorithm, and the cophenetic correlation coefficient calculated using the R software. The distance between the putative mutants ranged from 0.321 to 0.524, with an average distance of 0.426, and a cophenetic correlation coefficient of 0.79. Three putative mutants, which were selected based on the best agronomic traits and low height, will undergo further evaluation in the next stages of the banana breeding program at Embrapa. These results describe the first attempt of using combined data of Terra Maranhão plantain cultivar for the purpose of selecting mutants and assessing genetic variability.

Descriptor selection for banana accessions based on univariate and multivariate analysis

Our objective was to establish a minimum number of morphological descriptors for the characterization of banana germplasm and evaluate the efficiency of removal of redundant characters, based on univariate and multivariate statistical analyses. Phenotypic characterization was made of 77 accessions from Bahia, Brazil, using 92 descriptors. The selection of the descriptors was carried out by principal components analysis (quantitative) and by entropy (multi-category). Efficiency of elimination was analyzed by a comparative study between the clusters formed, taking into consideration all 92 descriptors and smaller groups. The selected descriptors were analyzed with the Ward-MLM procedure and a combined matrix formed by the Gower algorithm. We were able to reduce the number of descriptors used for characterizing the banana germplasm (42%). The correlation between the matrices considering the 92 descriptors and the selected ones was 0.82, showing that the reduction in the number of descriptors did not influence estimation of genetic variability between the banana accessions. We conclude that removing these descriptors caused no loss of information, considering the groups formed from pre-established criteria, including subgroup/subspecies.

Use of morpho-agronomic traits and DNA profiling for classification of genetic diversity in papaya

We examined the genetic diversity of papaya (Carica papaya) based on morpho-agronomic and molecular data. Twenty-seven genotypes grown in Brazil were analyzed with 11 AFLP primer combinations, 23 ISSR markers, 22 qualitative, and 30 quantitative descriptors. For the joint analyses, we used the Gower algorithm (Joint Gower) and the average value of the individual dissimilarity matrix for each type of data (Average-Joint Gower); 359 AFLP and 52 ISSR polymorphic bands were found. Approximately 29.2 and 7.7% of the AFLP and ISSR bands, respectively, were genotype-specific and may therefore be used for papaya variety protection. Although there was a significant correlation between the qualitative and quantitative descriptor dissimilarity matrices (r = 0.43), the morpho-agronomic data were not highly correlated with the molecular data. Moreover, correlation between AFLP and ISSR dissimilarity matrices was nearly null (r = -0.01). Joint Gower analysis of all data showed high correlations, especially for AFLP markers, most likely due to the larger number of bands, generating a strong bias in the diversity estimates. The Average-Joint Gower analysis allowed a better balance between the correlations for the continuous and the discrete variables. The results generated by clustering analysis distinguished 5 genetically distinct groups. While we found that papaya genotypes are significantly variable for many traits, we observed that Average-Joint Gower analysis allowed for genotype clustering based on the most widely used criterion for classifying papaya genotypes, which is fruit type ('Formosa' or 'Solo'). This information helps provide an accurate estimate of the genetic diversity and structure of papaya germplasm, which will be used for further breeding strategies.

Genetic diversity between improved banana diploids using canonical variables and the Ward-MLM method

The objective of this work was to estimate the genetic diversity of improved banana diploids using data from quantitative analysis and from simple sequence repeats (SSR) marker, simultaneously. The experiment was carried out with 33 diploids, in an augmented block design with 30 regular treatments and three common ones. Eighteen agronomic characteristics and 20 SSR primers were used. The agronomic characteristics and the SSR were analyzed simultaneously by the Ward-MLM, cluster, and IML procedures. The Ward clustering method considered the combined matrix obtained by the Gower algorithm. The Ward-MLM procedure identified three ideal groups (G1, G2, and G3) based on pseudo-F and pseudo-t² statistics. The dendrogram showed relative similarity between the G1 genotypes, justified by genealogy. In G2, 'Calcutta 4' appears in 62% of the genealogies. Similar behavior was observed in G3, in which the 028003-01 diploid is the male parent of the 086079-10 and 042079-06 genotypes. The method with canonical variables had greater discriminatory power than Ward-MLM. Although reduced, the genetic variability available is sufficient to be used in the development of new hybrids.